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Chapter 1

The Evolution of Microorganisms

and Microbiology

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The Importance of
Microorganisms
• most populous and diverse group of organisms
• found everywhere on the planet
• play a major role in recycling essential
elements
• source of nutrients and some carry out
photosynthesis
• benefit society by their production of food,
beverages, antibiotics, and vitamins
• some cause disease in plants and animals

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Members of the Microbial

World
• organisms and acellular entities too
small to be clearly seen by the
unaided eye
– some < 1 mm, some macroscopic
• these organisms are relatively simple
in their construction and lack highly
differentiated cells and distinct
tissues
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Figure 1.1
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Type of Microbial Cells

• prokaryotic cells lack a true
membrane-delimited nucleus
– This is not absolute
• eukaryotic cells have a membrane-
enclosed nucleus, are more complex
morphologically, and are usually
larger than prokaryotic cells
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Classification Schemes
• three domain system, based on a
comparison of ribosomal RNA,
divides microorganisms into
– Bacteria (true bacteria),
– Archaea
– Eukarya (eukaryotes)

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Domain Bacteria
• Usually single-celled
• Majority have cell wall with
peptidoglycan
• Most lack a membrane-bound nucleus
• Ubiquitous and some live in extreme
environments
• Cyanobacteria produce significant
amounts of oxygen
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Domain Archaea
• distinguished from Bacteria by
unique rRNA sequences
• lack peptidoglycan in cell walls
• have unique membrane lipids
• some have unusual metabolic
characteristics
• many live in extreme environments
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Figure 1.2 Universal Phylogenetic Tree

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Domain Eukarya - Eukaryotic

• protists – generally larger than Bacteria
and Archaea
– algae – photosynthetic
– protozoa – may be motile, “hunters, grazers”
– slime molds – two life cycle stages
– water molds – devastating disease in plants
• fungi
– yeast - unicellular
– mold - multicellular
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Acellular Infectious Agents

• viruses
– smallest of all microbes
– requires host cell to replicate
– cause range of diseases, some cancers
• viroids and virusoids
– infectious agents composed of RNA
• prions – infectious proteins
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 How is “Life” Defined?
Life:
– cells and organization
– energy use and metabolism
– response to environmental changes
– regulation and homeostasis
– growth and development
– biological evolution
– reproduction
Figure 1.3
 Origins of Life

• microbial fossils first found in 1977

– Swartkoppie chert – granular silica
– 3.5 billion years old
• fossil record sparse
• indirect evidence and scientific method
are used to study origins of life
Figure 1.5
Figure 1.6
 Earliest Molecules - RNA
• original molecule must have fulfilled
protein and hereditary function
• ribozymes
– RNA molecules that form peptide
bonds
– perform cellular work and replication
• earliest cells may have been RNA
surrounded by liposomes
 Earliest Molecules – RNA
• cellular pool of RNA in modern day cells
exists in and is associated with the
ribosome (rRNA, tRNA, mRNA)
– RNA catalytic in protein synthesis
– RNA may be precursor to double stranded
DNA
• Adenosine 5’ triphosphate (ATP) is the
energy currency and is a ribonucleotide
• RNA can regulate gene expression
Figure 1.7
 Earliest Metabolism
• early energy sources under harsh
conditions
– inorganics, e.g., FeS
• photosynthesis
– cyanobacteria evolved 2.5 billion ya
– stromatolites – mineralized layers of
microorganisms
Evolution of 3 Domains of Life
• universal phylogenetic tree
– based on comparisons of small subunit
rRNA (SSU rRNA)
– aligned rRNA sequences from diverse
organisms are compared and
differences counted to derive a value of
evolutionary distance
– relatedness, but not time of divergence,
is determined this way
Figure 1.9
 Last Universal Common
Ancestor (LUCA)
• the root or origin of modern life is on
bacterial branch but nature still
controversial
• Archaea and Eukarya evolved
independently of Bacteria
• Archaea and Eukarya diverged from
common ancestry
Endosymbiotic Hypothesis
• Endosymbiosis is the interaction of two
organisms in which one organism lives
within the other
• origin of mitochondria, chloroplasts, and
hydrogenosomes from endosymbiont
• mitochondria and chloroplasts
– SSU rRNA show bacterial lineage
– genome sequences closely related to
Richettsia and Prochloron, respectively
• hydrogenosomes
– anaerobic endosymbiont
Evolution of Cellular Microbes

• mutation of genetic material led to

selected traits
• new genes and genotypes evolved
• Bacteria and Archaea increase
genetic pool by horizontal gene
transfer within the same generation
 Microbial Species
• eukaryotic microbes fit definition of
reproducing isolated populations
• Bacteria and Archaea do not reproduce
sexually and are referred to as strains
– strain consists of descendents of a single,
pure microbial culture
– may be biovars, serovars, morphovars,
pathovars
• binomial nomenclature
– genus and species epithet
 Microbiology
• study of microorganisms
• tools used for the study
– microscopes
– culture techniques
– molecular genetics
– genomics
Figure 1.10
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Discovery of Microorganisms
• Antony van
Leeuwenhoek (1632-
1723) Figure 1.11 (a)
– first person to
observe and describe
microorganisms
accurately

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Figure 1.11 (b) and (c)

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The Conflict over

Spontaneous Generation
• spontaneous generation
– living organisms can develop from
nonliving or decomposing matter
• Francesco Redi (1626-1697)
– discredited spontaneous generation
– showed that maggots on decaying meat
came from fly eggs
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But Could Spontaneous Generation

Be True for Microorganisms?
• John Needham (1713-1781)
– his experiment:
mutton broth in flasks → boiled →sealed
– results: broth became cloudy and contained
microorganisms
• Lazzaro Spallanzani (1729-1799)
– his experiment:
broth in flasks →sealed → boiled
– results: no growth of microorganisms
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Louis Pasteur (1822-1895)

• his experiments
– placed nutrient solution in flasks
– created flasks with long, curved necks
– boiled the solutions
– left flasks exposed to air
• results: no growth of microorganisms

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Louis Pasteur (1822-1895)

Figure 1.12

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Figure 1.13
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Final Blow to Theory of

Spontaneous Generation
• John Tyndall (1820-1893)
– demonstrated that dust carries microorganisms
– showed that if dust was absent, nutrient broths
remained sterile, even if directly exposed to air
– also provided evidence for the existence of
exceptionally heat-resistant forms of bacteria
• Ferdinand Cohn (1828-1898)
– heat resistant bacteria could produce
endospores
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The Role of
Microorganisms in Disease
• was not immediately obvious
• infectious disease believed to be due
to supernatural forces
• establishing connection depended on
development of techniques for
studying microbes
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Evidence for the Relationship

between Microorganisms and
Disease
• Agostini Bassi (1773-1856)
– showed that a disease of silkworms was caused by a
fungus
• M. J. Berkeley (ca. 1845)
– demonstrated that the great Potato Blight of Ireland
was caused by a water mold
• Heinrich de Bary (1853)
– showed that smut and rust fungi caused cereal crop
diseases
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More Evidence…
• Louis Pasteur
– demonstrated microorganisms carried out
fermentations
– developed pasteurization
– showed that the pébrine disease of
silkworms was caused by a protozoan

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Other Evidence…
• Joseph Lister
– provided indirect evidence that
microorganisms were the causal agents of
disease
– developed a system of surgery designed to
prevent microorganisms from entering
wounds as well as methods for treating
instruments and surgical dressings
– his patients had fewer postoperative
infections
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Final Proof…
• Robert Koch (1843-1910)
– established the relationship between Bacillus
anthracis and anthrax
– used criteria developed by his teacher Jacob
Henle (1809-1895)
– these criteria now known as Koch’s
postulates
• still used today to establish the link between a
particular microorganism and a particular
disease

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Figure 1.14

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Koch’s Postulates
• the microorganism must be present in
every case of the disease but absent from
healthy individuals
• the suspected microorganism must be
isolated and grown in a pure culture
• the same disease must result when the
isolated microorganism is inoculated into
a healthy host
• the same microorganism must be isolated
again from the diseased host
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 Limitations of Koch’s
Postulated
• some organisms cannot be grown in
pure culture
• using humans in completing the
postulates is unethical
• molecular and genetic evidence may
replace
Figure 1.15
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The Development of
Techniques for Studying
Microbial Pathogens
• Koch’s work led to discovery or
development of:
– agar
– petri dish
– nutrient broth and nutrient agar
– methods for isolating microorganisms
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Other Developments…
• Charles Chamberland (1851-1908)
– developed porcelain bacterial filters used by
Ivanoski and Beijerinck to study tobacco
mosaic disease
• determined that extracts from diseased plants
had infectious agents present which were smaller
than bacteria and passed through the filters
• infectious agents were eventually shown to be
viruses

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Other Developments…
• Pasteur and Roux
– discovered that incubation of cultures
for long intervals between transfers
caused pathogens to lose their ability to
cause disease
• Pasteur and his coworkers
– developed vaccines for chicken cholera,
anthrax, and rabies

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Immunological Studies
• once established, led to study of host
defenses - immunology
• Edward Jenner (ca. 1798)
– used a vaccination procedure to
protect individuals from smallpox
NOTE: this preceded the work establishing
the role of microorganisms in disease

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More Developments…
• Emil von Behring (1854-1917) and
Shibasaburo Kitasato (1852-1931)
– developed antitoxins for diphtheria and
tetanus
– evidence for humoral immunity
• Elie Metchnikoff (1845-1916)
– discovered bacteria-engulfing, phagocytic
cells in the blood
– evidence for cellular immunity

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The Development of Industrial

Microbiology and Microbial
Ecology
• Louis Pasteur
– demonstrated that alcohol
fermentations and other fermentations
were the result of microbial activity
– developed the process of pasteurization
to preserve wine during storage
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Developments in Microbial
Ecology
• Sergei Winogradsky (1856-1953) and
Martinus Beijerinck (1851-1931)
– studied soil microorganisms and discovered
numerous interesting metabolic processes
(e.g., nitrogen fixation)
– pioneered the use of enrichment cultures and
selective media

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Microbiology Has Basic and

Applied Aspects
• basic aspects are concerned with
individual groups of microbes, microbial
physiology, genetics, molecular biology
and taxonomy
• applied aspects are concerned with
practical problems – disease, water, food
and industrial microbiology
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 Major Fields in Microbiology

• medical microbiology – diseases of

humans and animals
• public health microbiology – control
and spread of communicable diseases
• immunology – how the immune
system protects a host from
pathogens
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More Fields…
• microbial ecology is concerned with the
relationship of organisms with their
environment
– less than 1% of earth’s microbial population
has been cultured
• agricultural microbiology is concerned
with the impact of microorganisms on
agriculture
– food safety microbiology
– animal and plant pathogens
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 More Fields….
• industrial microbiology began in the
1800s
– fermentation
– antibiotic production
– production of cheese, bread, etc.
• microbial physiology studies
metabolic pathways of
microorganisms
 More Fields….
• molecular biology, microbial
genetics, and bioinformatics study
the nature of genetic information
and how it regulates the
development and function of cells
and organisms
• microbes are a model system of
genomics